Beginner: Wrong workflow? 8x8x8 LED Cube to complex
I honestly see no problem with this, there is not much you can do except
for making the mesh at a lower resolution, 
you do not mention what engine you are using this in, but one option might be to look in the engine you use, then see if it supports instancing of meshes which then can have separate materials assigned (I assume you are assigning materials to the different LED's during runtime.).

The you only export one LED, then create it all by code (instance,move the instance, assign materials and so on). That way the mesh memory is kept low, because it will only load 1 LED mesh.

But again - this scene is not big at all compared to other game content that typically exists in a scene.